Investigation of Pathogenic to Benign Reclassifications - Expert Curated Dataset
Analysis of excluded P→B variants and special notes for included variants.
Distribution of validated P→B reclassifications across genes and their characteristics.
Temporal patterns in validated variant reclassifications.
Inferred reasons driving validated P→B reclassifications based on ACMG evidence codes.
Analysis of submitter patterns in validated reclassifications.
The time between initial pathogenic classification and benign reclassification spans years, with a median of approximately 6 years. This lag represents a critical window where patients may receive inaccurate genetic counseling.
Summary Statistics:
Population frequency evidence (BA1/BS1) is the dominant driver of pathogenic-to-benign reclassifications. As large-scale population databases like gnomAD have grown, variants once thought rare enough to be pathogenic are now recognized as benign polymorphisms.
BA1/BS1 prevalence increased dramatically from 0.0% on the P/LP side to 50.0% on the B/LB side.
Fisher's Exact Test: Odds Ratio = inf, p-value = 1.84e-04
The evolution from the 2015 ACMG/AMP guidelines to gene-specific VCEP (Variant Curation Expert Panel) specifications has fundamentally changed how evidence is weighted and interpreted.
Approximately 22.7% of reclassifications involve both a change in guideline and a shift in evidence bucket composition, highlighting the impact of gene-specific VCEP specifications.
| Framework | Key Changes | Example Genes |
|---|---|---|
| ACMG 2015 (generic) | One-size-fits-all evidence codes | All genes |
| BRCA1/2 ENIGMA (2020) | Adjusted functional assay thresholds, refined splicing rules | BRCA1, BRCA2 |
| TSC1/2 Zhou (2019) | LOF mechanism-specific criteria | TSC1, TSC2 |
| Kidney VCEP (in development) | Disease-specific population frequency thresholds | PKD1, PKD2, COL4A5 |
Computational prediction tools (PP3 for pathogenic, BP4 for benign) are inherently unstable. As algorithms are retrained on new data or replaced with newer models, the same variant can flip from computationally predicted pathogenic to benign.
Computational evidence shifted in 5 variants with PP3 (P/LP side) and 10 variants with BP4 (B/LB side). Below are case studies where the same variant went from PP3-supported pathogenic to BP4-supported benign:
| Gene | Variant | Time (mo) | P/LP Date | P/LP Submitter | P/LP Codes | B/LB Date | B/LB Submitter | B/LB Codes |
|---|---|---|---|---|---|---|---|---|
| BRCA2 | NM_000059.4(BRCA2):c.8851G>T (p.Ala2951S... | 61.2 | 2020-04-08 | Center of Medical Genetic | PM1,PM2,PP3,PP4 | 2025-05-16 | Ambry Genetics | BP2,BP4,BP5,BP7,BS1,BS2,BS3,BS |
| NPHS1 | NM_004646.4(NPHS1):c.559G>A (p.Val187Met... | 53.5 | 2018-09-16 | Gharavi Laboratory, Colum | PM2,PP3,PP4 | 2023-03-02 | Labcorp Genetics (formerl | BA1,BP4,BS1 |
| TSC2 | NM_000548.5(TSC2):c.4639G>A (p.Val1547Il... | 45.3 | 2017-04-11 | OMIM | PM2,PP3,PS3 | 2021-01-19 | Ambry Genetics | BP1,BP4,BP5,BS1,BS2,BS3,BS4 |
| PAX2 | NM_000278.5(PAX2):c.1058A>C (p.Gln353Pro... | nan | N/A | Precision Medicine Center | PM1,PP1,PP3,PP4,PP5 | 2020-01-22 | PreventionGenetics, part | BP4,BP7,BS1 |
Functional evidence is often treated as highly reliable (PS3 for pathogenic functional studies, BS3 for benign). However, the data show that variants with PS3 evidence can later acquire BS3 evidence, suggesting that single functional assays may be insufficient or that assay conditions matter greatly.
Functional evidence reversed in 2 variants with PS3 (P/LP side) and 3 variants with BS3 (B/LB side). Below are case studies where functional assays contradicted each other:
| Gene | Variant | Time (mo) | P/LP Date | P/LP Submitter | P/LP Codes | B/LB Date | B/LB Submitter | B/LB Codes |
|---|---|---|---|---|---|---|---|---|
| TSC2 | NM_000548.5(TSC2):c.4639G>A (p.Val1547Il... | 45.3 | 2017-04-11 | OMIM | PM2,PP3,PS3 | 2021-01-19 | Ambry Genetics | BP1,BP4,BP5,BS1,BS2,BS3,BS4 |
| Era/Standard | Typical Assay | Limitations | Modern Approach |
|---|---|---|---|
| Legacy PS3 (single-variant) | Cell viability, Western blot, localization | Small N, variable conditions, publication bias | — |
| Current BS3 (validated, multiplex) | MAVEs, HDR assays, orthogonal validation | — | Assay validation, controls, reproducibility |
Complete list of validated P→B variants with classification details and inferred reclassification reasons.
Showing 22 validated P→B variants (exclude=false) sorted by gene and time to reclassification. Table is scrollable.
| gene | variant | type | first_plp_date | first_blb_date | first_plp_submitter | first_blb_submitter | time_to_benign_months | interlab | plp_codes | blb_codes | inferred_reasons | exclude_reason |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BRCA2 | NM_000059.4(BRCA2):c.8187G>T (p.Lys2729Asn) | missense | 2002-07-26 | 2011-03-14 | OMIM | Sharing Clinical Reports Project (SCRP) | 103.6 | True | Other/Unknown | Special Note: A submission from the Online Mendelian Inheritance in Man (OMIM) for this variant is associated with a disease identifier that was once considered pathogenic. However, this does not mean that OMIM submitted a classification of pathogenic for this specific variant. The reason is a known discrepancy in how OMIM data was historically displayed on ClinVar. | ||
| BRCA2 | NM_000059.4(BRCA2):c.7879A>T (p.Ile2627Phe) | missense | 2012-03-11 | 2019-09-01 | Sharing Clinical Reports Project (SCRP) | King Laboratory, University of Washington | 89.7 | True | Other/Unknown | Special Note: This variants has a complcated history of calssifications. Although the ClinGen Expert Panel classified it as Pathogenic for BRCA2-related cancer predisposition on 2024/06/11, there is a hiden record in vcv xml file saying a new submitter submitted the classification as benign on 2025/09/07 (ClinVar might not have time to review and update it). Also in its publically shown history record, King Laboratory, Univeristy of Washington classified it as Benign on 2019/09/01 with a cited publication. | ||
| BRCA2 | NM_000059.4(BRCA2):c.891_899delinsGATACTTAG (p.Thr298_Val300delinsIleLeuArg) | missense | 2017-04-20 | 2023-03-23 | Department of Pathology and Molecular Medicine, Queen's University | University of Washington Department of Laboratory Medicine, University of Washington | 71.1 | True | PM1,PM2,PP4 | BP1 | Guideline/model change | N/A |
| BRCA2 | NM_000059.4(BRCA2):c.8851G>T (p.Ala2951Ser) | missense | 2020-04-08 | 2025-05-16 | Center of Medical Genetics and Primary Health Care | Ambry Genetics | 61.2 | True | PM1,PM2,PP3,PP4 | BP2,BP4,BP5,BP7,BS1,BS2,BS3,BS4 | Population frequency, New benign functional evidence, Computational shift | N/A |
| BRCA2 | NM_000059.4(BRCA2):c.2623G>C (p.Val875Leu) | missense | 2020-04-08 | 2023-03-23 | Center of Medical Genetics and Primary Health Care | University of Washington Department of Laboratory Medicine, University of Washington | 35.4 | True | BP4,PM1,PM2,PP1,PS1 | BP4,BS1 | Population frequency, Guideline/model change | N/A |
| COL4A5 | NM_033380.3(COL4A5):c.2692A>G (p.Met898Val) | missense | 2019-02-14 | 2019-06-15 | Yale Center for Mendelian Genomics, Yale University | PreventionGenetics, part of Exact Sciences | 4.0 | True | Other/Unknown | N/A | ||
| HNF1A | NM_000545.8(HNF1A):c.1748G>A (p.Arg583Gln) | missense | 2002-10-01 | 2016-10-27 | OMIM | Ambry Genetics | 168.9 | True | BP1,BP4,BP5,BS1,BS2,BS3,BS4 | Population frequency, New benign functional evidence | N/A | |
| HNF1A | NM_000545.8(HNF1A):c.92G>A (p.Gly31Asp) | missense | 2005-03-01 | 2017-03-01 | OMIM | GeneDx | 144.0 | True | BP4,BS1 | Population frequency | N/A | |
| NPHS1 | NM_004646.4(NPHS1):c.559G>A (p.Val187Met) | Missense variant in extracellular domain of nephrin protein | 2018-09-16 | 2023-03-02 | Gharavi Laboratory, Columbia University | Labcorp Genetics (formerly Invitae), Labcorp | 53.5 | True | PP4 | Other/Unknown | N/A | |
| NPHS1 | NM_004646.4(NPHS1):c.559G>A (p.Val187Met) | missense | 2018-09-16 | 2023-03-02 | Gharavi Laboratory, Columbia University | Labcorp Genetics (formerly Invitae), Labcorp | 53.5 | True | PM2,PP3,PP4 | BA1,BP4,BS1 | Population frequency (BA1 threshold), Computational shift, Guideline/model change | N/A |
| NPHS1 | NM_004646.4(NPHS1):c.559G>A (p.Val187Met) | missense | 2018-09-16 | 2023-03-02 | Gharavi Laboratory, Columbia University | Labcorp Genetics (formerly Invitae), Labcorp | 53.5 | True | Other/Unknown | N/A | ||
| NPHS2 | NM_014625.4(NPHS2):c.59C>T (p.Pro20Leu) | missense | 2003-05-01 | 2016-03-04 | OMIM | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | 154.1 | True | PM1,PM2,PP1,PS4 | BP4,BP6,BS1,BS2 | Population frequency | Special Note: variant was initially considered pathogenic. This early classification, however, has since been re-evaluated and corrected based on further research and genetic analysis. |
| NPHS2 | NM_014625.4(NPHS2):c.59C>T (p.Pro20Leu) | missense | 2003-05-01 | 2016-03-04 | OMIM | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | 154.1 | True | BS1,BS2 | Population frequency | Special Note: Initial association with disease (2000s): Early studies, including one in 2000, identified this variant in patients with steroid-resistant nephrotic syndrome. | |
| PAX2 | NM_000278.5(PAX2):c.1058A>C (p.Gln353Pro) | missense | 2020-01-22 | Precision Medicine Center, Zhengzhou University | PreventionGenetics, part of Exact Sciences | NaN | True | PM1,PP1,PP3,PP4,PP5 | BP4,BP7,BS1 | Population frequency, Computational shift, Guideline/model change | Special Note: The Likely pathogenic submission is a flagged submission, with reason of claim with insufficient supporting evidence. From ClinVar, it says Explanation for multiple conditions: Uncertain. The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. | |
| PAX2 | NM_000278.5(PAX2):c.1058A>C (p.Gln353Pro) | missense | 2020-01-22 | Precision Medicine Center, Zhengzhou University | PreventionGenetics, part of Exact Sciences | NaN | True | PM1,PP1,PP3,PP4,PP5 | Other/Unknown | N/A | ||
| PKD1 | NM_001009944.3(PKD1):c.971G>T (p.Arg324Leu) | missense | 1999-07-01 | 2019-04-19 | OMIM | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | 237.6 | True | Other/Unknown | N/A | ||
| PKD1 | NM_001009944.3(PKD1):c.971G>T (p.Arg324Leu) | missense | 1999-07-01 | 2019-04-19 | OMIM | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | 237.6 | True | Other/Unknown | N/A | ||
| RET | NM_020975.6(RET):c.2372A>T (p.Tyr791Phe) | missense | 2006-08-28 | 2012-07-13 | Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital | Biesecker Lab/Clinical Genomics Section, National Institutes of Health | 70.5 | True | Other/Unknown | N/A | ||
| SCNN1G | NM_001039.4(SCNN1G):c.589G>A (p.Glu197Lys) | missense | 2008-05-28 | 2017-04-27 | OMIM | Illumina Laboratory Services, Illumina | 107.0 | True | PP1,PS3 | BP4,BS1 | Population frequency | N/A |
| SCNN1G | NM_001039.4(SCNN1G):c.589G>A (p.Glu197Lys) | missense | 2008-05-28 | 2017-04-27 | OMIM | Illumina Laboratory Services, Illumina | 107.0 | True | BS1 | Population frequency | N/A | |
| TSC2 | NM_000548.5(TSC2):c.4639G>A (p.Val1547Ile) | missense | 2017-04-11 | 2021-01-19 | OMIM | Ambry Genetics | 45.3 | True | PM2,PP3,PS3 | BP1,BP4,BP5,BS1,BS2,BS3,BS4 | Population frequency, Functional (benign evidence), Computational shift | N/A |
| TSC2 | NM_000548.5(TSC2):c.1081C>G (p.Leu361Val) | missense | 2018-08-01 | 2020-03-20 | Liping Wei Laboratory, Peking University | GeneDx | 19.6 | True | BP4,BS4 | Guideline/model change | N/A |